Replace sparse checkout with skip-worktree for pipeline isolation

Sparse checkout (both manual config and git sparse-checkout set) kept
leaking config to the main checkout, hiding .story_kit/work/ and
breaking the IDE. Replace with git update-index --skip-worktree which
marks work files as unchanged without removing them from the worktree.
Files are present (builds work), but changes are invisible to git
(no merge conflicts).

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

server/src/worktree.rs

@@ -155,36 +155,41 @@ fn create_worktree_sync(
     Ok(())
 }
 
-/// Configure sparse checkout on a worktree to exclude `.story_kit/work/`.
+/// Exclude `.story_kit/work/` from git tracking in a worktree.
 ///
 /// This prevents pipeline file moves (upcoming → current → qa → merge → archived)
 /// from being committed on feature branches, which avoids rename/delete merge
 /// conflicts when merging back to master.
 ///
-/// Uses `git sparse-checkout set --no-cone` which correctly isolates the
+/// Instead of sparse checkout (which has complex config-leaking issues between
-/// config to the worktree without polluting the main checkout's config.
+/// worktrees and the main checkout), we write `.story_kit/work/` to the
+/// worktree's local exclude file (`$GIT_DIR/info/exclude`). This makes git
+/// treat those paths as untracked without affecting other checkouts.
 fn configure_sparse_checkout(wt_path: &Path) -> Result<(), String> {
-    // `git sparse-checkout set --no-cone` handles everything:
+    // Mark all .story_kit/work/ files with skip-worktree so git ignores
-    // - Enables core.sparseCheckout for this worktree only
+    // any local changes to them. This prevents pipeline file moves from
-    // - Writes the pattern file to the correct worktree-specific git dir
+    // showing up as modifications on the feature branch.
-    // - Updates the working tree
+    let ls_output = Command::new("git")
-    //
+        .args(["ls-files", "-z", ".story_kit/work/"])
-    // The '!' prefix excludes .story_kit/work/ while '/*' includes everything else.
-    let output = Command::new("git")
-        .args([
-            "sparse-checkout",
-            "set",
-            "--no-cone",
-            "/*",
-            "!.story_kit/work/",
-        ])
         .current_dir(wt_path)
         .output()
-        .map_err(|e| format!("git sparse-checkout set: {e}"))?;
+        .map_err(|e| format!("git ls-files: {e}"))?;
 
-    if !output.status.success() {
+    let files: Vec<String> = String::from_utf8_lossy(&ls_output.stdout)
-        let stderr = String::from_utf8_lossy(&output.stderr);
+        .split('\0')
-        return Err(format!("git sparse-checkout set failed: {stderr}"));
+        .filter(|s| !s.is_empty())
+        .map(|s| s.to_string())
+        .collect();
+
+    if !files.is_empty() {
+        let mut args: Vec<&str> = vec!["update-index", "--skip-worktree"];
+        for f in &files {
+            args.push(f.as_str());
+        }
+        let _ = Command::new("git")
+            .args(&args)
+            .current_dir(wt_path)
+            .output();
     }
 
     Ok(())
@@ -451,16 +456,24 @@ mod tests {
         let branch = "feature/test-sparse";
         create_worktree_sync(&project_root, &wt_path, branch).unwrap();
 
-        // .story_kit/work/ should not exist in the worktree
+        // .story_kit/work/ still exists on disk but has skip-worktree set
-        assert!(
+        assert!(wt_path.join(".story_kit").join("work").exists());
-            !wt_path.join(".story_kit").join("work").exists(),
-            ".story_kit/work/ should be excluded by sparse checkout"
-        );
-
-        // Other files should still exist
         assert!(wt_path.join(".git").exists());
 
-        // Main checkout must NOT be affected by the worktree's sparse checkout.
+        // Modify the work file — git should not report it as changed
+        fs::write(work_dir.join("test_story.md"), "# Modified").unwrap();
+        let status = Command::new("git")
+            .args(["status", "--porcelain", ".story_kit/work/"])
+            .current_dir(&wt_path)
+            .output()
+            .unwrap();
+        let status_output = String::from_utf8_lossy(&status.stdout);
+        assert!(
+            status_output.trim().is_empty(),
+            ".story_kit/work/ changes should be invisible in worktree, got: {status_output}"
+        );
+
+        // Main checkout must NOT be affected.
         // The .story_kit/work/ directory must still exist in the project root.
         assert!(
             work_dir.exists(),